.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2702_54x886_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Compute approximate likelihood ratio test : yes (SH-like branch supports) . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : no . Evaluted tree : file "user tree (RAxML_result.nucleic_M2702_54x886_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 2 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 382 patterns found. (out of a total of 886 sites) . 582 sites without polymorphism (65.69%). . Reading tree... . This analysis requires at least 11Mo of memory space. . ( 0 sec) [ -5800.5379] [Branch lengths ] . ( 2 sec) [ -5521.3817] [GTR parameters ] . ( 2 sec) [ -5432.6151] [Alpha ][ 0.500960] . ( 2 sec) [ -5427.9200] [Branch lengths ] . ( 3 sec) [ -5427.4340] [GTR parameters ] . ( 3 sec) [ -5385.3603] [Alpha ][ 0.250961] . ( 4 sec) [ -5383.8160] [Branch lengths ] . ( 5 sec) [ -5383.0045] [GTR parameters ] . ( 5 sec) [ -5382.7513] [Alpha ][ 0.238580] . ( 5 sec) [ -5382.4571] [Branch lengths ] . ( 6 sec) [ -5382.4398] [GTR parameters ] . ( 6 sec) [ -5382.4398] [Alpha ][ 0.238580] . ( 6 sec) [ -5382.3772] [Branch lengths ] . ( 6 sec) [ -5382.3761] [GTR parameters ] . ( 7 sec) [ -5382.3760] [Alpha ][ 0.238818] . ( 7 sec) [ -5382.3643] [Branch lengths ] . ( 7 sec) [ -5382.3640] [GTR parameters ] . ( 7 sec) [ -5382.3640] [Alpha ][ 0.238818] . ( 8 sec) [ -5382.3617] [Branch lengths ] . ( 8 sec) [ -5382.3616] [GTR parameters ] . ( 8 sec) [ -5382.3616] [Alpha ][ 0.238818] . ( 8 sec) [ -5382.3612] [Branch lengths ] . ( 9 sec) [ -5382.3612] [GTR parameters ] . ( 9 sec) [ -5382.3612] [Alpha ][ 0.238818] . ( 9 sec) [ -5382.3612] [GTR parameters ] . ( 9 sec) [ -5382.3612] [Alpha ][ 0.238818] . Log likelihood of the current tree: -5382.361164. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2702_54x886_2006.phy_phyml_tree.txt'... . Time used 0h0m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo java.lang.NullPointerException at java.io.FileInputStream.(FileInputStream.java:103) at java.io.FileReader.(FileReader.java:55) at Recomp.(Recomp.java:114) at Recomp.main(Recomp.java:52)